I have not heard from any of the programs (Physics PhD) I applied to yet. My thoughts on the effect of a brief email to the graduate coordinator are:
Pros — The admission committee at the graduate program will have the knowledge that another committee (for a prestigious scholarship) has reviewed my project/profile/etc and found me of a high caliber.
Cons — The admission committee may be annoyed by my contact, viewing me as trying to score some "brownie points." It is only semi-finalist, I still have to be selected in the final round.